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CRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN (TM1389) FROM THERMOTOGA MARITIMA MSB8 AT 2.35 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5 293 1.0M LiCl, 10.0% PEG-600, 0.1M Citrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.0 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 7 293 40.0% MPD, 0.1M HEPES, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.475 α = 90 b = 130.475 β = 90 c = 192.926 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2005-07-04 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 flat mirror 2005-06-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979318, 0.918370 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 2.35 29.8 99.6 0.183 0.183 3.4 9.8 40826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.35 2.41 95.3 0.981 0.981 0.7 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.35 29.8 38735 2048 99.69 0.171 0.169 0.1794 0.199 0.2039 RANDOM 44.977
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.91 0.96 1.91 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 15.282 r_scangle_it 7.3 r_dihedral_angle_1_deg 6.452 r_scbond_it 5.32 r_mcangle_it 2.972 r_mcbond_it 2.165 r_angle_refined_deg 1.459 r_angle_other_deg 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 15.282 r_scangle_it 7.3 r_dihedral_angle_1_deg 6.452 r_scbond_it 5.32 r_mcangle_it 2.972 r_mcbond_it 2.165 r_angle_refined_deg 1.459 r_angle_other_deg 0.8 r_mcbond_other 0.529 r_symmetry_vdw_other 0.276 r_symmetry_vdw_refined 0.247 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.204 r_nbtor_refined 0.186 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3991 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling